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- PDB-2wv4: Crystal structure of foot-and-mouth disease virus 3C protease in ... -

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Basic information

Entry
Database: PDB / ID: 2wv4
TitleCrystal structure of foot-and-mouth disease virus 3C protease in complex with a decameric peptide corresponding to the VP1-2A cleavage junction
Components
  • FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN
  • PICORNAIN 3C
KeywordsHYDROLASE/PEPTIDE / HYDROLASE PEPTIDE COMPLEX / 3C PROTEASE / HYDROLASE / VIRAL PROTEIN / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / viral capsid / regulation of translation ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / viral capsid / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / viral protein processing / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFOOT-AND-MOUTH DISEASE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZunszain, P.A. / Knox, S.R. / Sweeney, T.R. / Yang, J. / Roque-Rosell, N. / Belsham, G.J. / Leatherbarrow, R.J. / Curry, S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Insights Into Cleavage Specificity from the Crystal Structure of Foot-and-Mouth Disease Virus 3C Protease Complexed with a Peptide Substrate.
Authors: Zunszain, P.A. / Knox, S.R. / Sweeney, T.R. / Yang, J. / Roque-Rosell, N. / Belsham, G.J. / Leatherbarrow, R.J. / Curry, S.
History
DepositionOct 13, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PICORNAIN 3C
B: PICORNAIN 3C
C: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN
D: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)48,3864
Polymers48,3864
Non-polymers00
Water59433
1
B: PICORNAIN 3C
D: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,1932
Polymers24,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-11.7 kcal/mol
Surface area9110 Å2
MethodPISA
2
A: PICORNAIN 3C
C: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,1932
Polymers24,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-10.9 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.760, 75.250, 85.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9696, 0.0779, 0.2321), (0.1688, 0.8994, 0.4032), (-0.1773, 0.4301, -0.8852)
Vector: -1.4313, -10.747, 31.2659)

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Components

#1: Protein PICORNAIN 3C / FOOT-AND-MOUTH DISEASE VIRUS 3C PROTEASE / PROTEASE 3C / P3C / PROTEASE P20B


Mass: 23049.654 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS / Strain: A10-61 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03306, picornain 3C
#2: Protein/peptide FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Mass: 1143.312 Da / Num. of mol.: 2 / Fragment: VP1-2A CLEAVAGE JUNCTION (P5-P5'), RESIDUES 29-38 / Source method: obtained synthetically / Source: (synth.) FOOT-AND-MOUTH DISEASE VIRUS / References: UniProt: Q65050, UniProt: P03306*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS1744 TO LYS ENGINEERED RESIDUE IN CHAIN A, CYS1791 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, CYS1744 TO LYS ENGINEERED RESIDUE IN CHAIN A, CYS1791 TO LEU ENGINEERED RESIDUE IN CHAIN A, CYS1812 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS1744 TO LYS ENGINEERED RESIDUE IN CHAIN B, CYS1791 TO LEU ENGINEERED RESIDUE IN CHAIN B, CYS1812 TO ALA
Has protein modificationY
Sequence detailsCONTAINS ADDITIONAL GLY AS RESIDUE 1. LAST 6 RESIDUES AT C- TERM MISSING FROM OUR STRUCTURE. ...CONTAINS ADDITIONAL GLY AS RESIDUE 1. LAST 6 RESIDUES AT C- TERM MISSING FROM OUR STRUCTURE. SEQUENCE DATABASE ENTRY FOR THIS PROTEIN CONTAINS KNOWN ERRORS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 7 / Details: SEE PAPER, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→30.3 Å / Num. obs: 14044 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.1
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.5 / % possible all: 78.5

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J92

2j92


Resolution: 2.5→29.74 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1028469.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 704 5 %RANDOM
Rwork0.212 ---
obs0.212 14014 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.6836 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 46.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.76 Å20 Å20 Å2
2---1.85 Å20 Å2
3---9.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 0 33 2991
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 88 4.7 %
Rwork0.28 1793 -
obs--77 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CAPPING.PARAMCAPPING.TOP

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